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. 2010 Oct 1;76(23):7775–7784. doi: 10.1128/AEM.01122-10

TABLE 2.

Expression ratio values of the genes showing largest regulatory responses to growth in mixed culturea

Category and locus tag Gene COG name Expression ratio (mixed culture/monoculture)
3.5 h 5.5 h 8 h 12 h
Folic acid metabolism
    LBUL_0208 Dihydroneopterin aldolase 0.88 0.43 1.28 2.25
    LBUL_0209 GTP cyclohydrolase I 0.40 0.32 1.35 1.64
    LBUL_0210 Folylpolyglutamate synthase 0.50 0.31 1.41 1.44
    LBUL_0211 Dihydropteroate synthase and related enzymes 0.69 0.39 1.39 2.30
    LBUL_0212 NTP pyrophosphohydrolases including oxidative damage repair enzymes 0.63 0.31 1.26 2.88
    LBUL_0660 Folylpolyglutamate synthase 0.69 0.37 0.78 4.82
Purine metabolism
    LBUL_0156 Phosphoribosylpyrophosphate synthetase 2.09 1.16 0.44 0.50
    LBUL_0246 IMP dehydrogenase/GMP reductase 0.24 0.30 1.27 0.05
    LBUL_0251 IMP dehydrogenase/GMP reductase 2.63 0.68 1.33 0.91
    LBUL_0252 GMP synthase PP-ATPase domain/subunit 2.32 0.94 1.57 1.60
    LBUL_0305 Phosphoribosylpyrophosphate synthetase 0.78 0.66 0.57 1.32
    LBUL_1330 Phosphoribosylamine-glycine ligase 0.99 0.37 1.18 0.06
    LBUL_1331 AICAR transformylase/IMP cyclohydrolase PurH (only IMP cyclohydrolase domain in Aful) 1.21 0.43 1.23 0.05
    LBUL_1332 Folate-dependent phosphoribosylglycinamide formyltransferase PurN 1.20 0.58 1.22 0.06
    LBUL_1333 Phosphoribosylaminoimidazole (AIR) synthetase 1.29 0.34 1.19 0.04
    LBUL_1334 Glutamine phosphoribosylpyrophosphate amidotransferase 1.25 0.37 1.28 0.05
    LBUL_1335 Phosphoribosylformylglycinamidine (FGAM) synthase synthetase domain 1.66 0.46 1.18 0.07
    LBUL_1336 Phosphoribosylformylglycinamidine (FGAM) synthase glutamine amidotransferase domain 0.96 0.44 0.92 0.04
    LBUL_1337 Phosphoribosylformylglycinamidine (FGAM) synthase PurS component 0.89 0.61 0.81 0.03
    LBUL_1338 Phosphoribosylaminoimidazolesuccinocarboxamide (SAICAR) synthase 0.83 0.64 0.88 0.03
    LBUL_1339 Adenylosuccinate lyase 1.79 1.78 0.85 0.17
    LBUL_1340 Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) 2.05 1.90 0.92 0.10
    LBUL_1341 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase 1.96 1.55 0.57 0.14
    LBUL_1754 GMP synthase-glutamine amidotransferase domain 1.21 0.59 1.52 1.78
    str0030 purC Phosphoribosylaminoimidazole-succinocarboxamide synthase 2.74 1.15 0.27 0.10
    str0031 purL Phosphoribosylformylglycinamidine synthase II (FGAM synthetase) 1.94 1.50 0.40 0.31
    str0031 purL Phosphoribosylformylglycinamidine synthase II (FGAM synthetase) 1.94 1.50 0.40 0.31
    str0032 purF Amidophosphoribosyltransferase 1.59 1.61 0.45 0.43
    str0033 purM Phosphoribosylaminoimidazole synthetase 1.54 1.64 0.48 0.47
    str0034 purN Phosphoribosylglycinamide formyltransferase 1.47 1.60 0.50 0.48
    str0035 purH Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase 1.86 2.18 0.47 0.70
    str0040 purD Phosphoribosylamine-glycine ligase 4.90 2.56 0.50 0.15
    str0041 purE Phosphoribosylaminoimidazole carboxylase catalytic subunit 5.76 4.05 0.79 0.20
    str0042 purK Phosphoribosylaminoimidazole carboxylase 5.41 3.90 0.77 0.31
    str0045 purB1 Adenylosuccinate lyase 2.23 2.08 0.53 0.37
    str1640 pflA Pyruvate-formate lyase activating enzyme 4.06 0.79 0.66 0.47
    str1657 pfl Pyruvate formate-lyase 3.03 1.38 0.97 0.76
BCAA metabolism
    LBUL_0077 l-2-Hydroxyisocaproate dehydrogenase 0.64 0.86 1.78 1.48
    LBUL_0392 Aspartate/tyrosine/aromatic aminotransferase 1.33 1.02 3.31 0.62
    LBUL_0431 Branched-chain amino acid permease 0.71 0.58 2.34 1.44
    LBUL_0659 Valyl-tRNA synthetase 1.08 0.43 1.27 6.46
    LBUL_0681 Isoleucyl-tRNA synthetase 0.94 0.62 1.74 4.51
    LBUL_1180 Aspartate/tyrosine/aromatic aminotransferase 1.15 1.21 0.51 1.13
    LBUL_1219 BCAA aminotransferase/4-amino-4-deoxychorismate lyase 0.64 0.63 0.56 4.74
    LBUL_1451 Leucyl-tRNA synthetase 0.86 0.41 0.87 3.54
    LBUL_2034 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase pyruvate dehydrogenase (cytochrome) glyoxylate carboligase phosphonopyruvate decarboxylase] 0.44 0.24 0.80 11.11
    str0220 leuS Leucyl-tRNA synthetase 2.13 1.95 2.17 1.22
    str0359 livJ BCAA ABC transporter substrate-binding protein 1.37 0.80 1.30 0.60
    str0360 livH BCAA ABC transporter permease protein 1.18 0.76 1.33 0.79
    str0361 livM BCAA ABC transporter permease protein 1.09 0.67 1.34 1.22
    str0362 livG BCAA ABC transporter ATP binding protein 2.00 1.14 1.03 1.49
    str0363 livF BCAA ABC transporter ATP binding protein 1.51 0.62 0.96 1.37
    str0477 valS Valyl-tRNA synthetase 1.03 0.83 3.59 4.89
    str0590 bcaT BCAA aminotransferase 2.01 1.18 0.78 0.30
    str0644 hdhL l-2-Hydroxyisocaproate dehydrogenase 1.14 1.11 1.15 3.24
    str0741 ileS Isoleucyl-tRNA synthetase 0.81 0.86 2.18 2.63
    str1357 brnQ BCAA transport system II carrier protein 0.51 0.59 1.44 0.28
    str1438 amiF1 Oligopeptide ABC transporter ATP-binding protein 0.49 0.39 2.75 0.72
    str1439 amiE Oligopeptide ABC transporter ATP-binding protein 0.61 0.23 2.46 0.62
    str1440 amiD Oligopeptide ABC transporter membrane-binding protein 0.45 0.14 2.73 0.55
    str1441 amiC Oligopeptide ABC transporter membrane-binding protein 0.50 0.30 2.79 0.39
    str1635 codY Transcriptional repressor CodY 1.01 0.76 0.59 1.02
Sulfur amino acid metabolism
    LBUL_0089 Homoserine trans-succinylase 0.61 0.46 0.76 0.21
    LBUL_0096 Methionine synthase II (cobalamin-independent) 2.66 0.84 2.71 1.24
    LBUL_0268 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) 2.48 0.79 3.03 0.93
    LBUL_0297 Methionyl-tRNA synthetase 1.81 0.91 1.11 2.24
    LBUL_0685 Adenosyl homosysteine nucleosidase 0.23 0.35 4.17 5.42
    LBUL_0686 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes 0.41 0.34 1.14 5.14
    LBUL_1103 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities 0.32 0.75 1.54 1.97
    LBUL_1232 Methionine synthase II (cobalamin-independent) 0.50 0.55 0.94 2.23
    LBUL_1235 Cysteine synthase 9.11 2.88 23.09 2.84
    LBUL_1236 Cystathionine beta-lyases/cystathionine gamma-synthases 6.30 2.85 13.94 4.31
    LBUL_1259 Homoserine dehydrogenase 0.93 0.93 1.84 1.02
    LBUL_1353 Homoserine trans-succinylase 0.50 0.27 0.59 0.08
    LBUL_1354 Cysteine synthase 0.69 0.21 0.36 0.03
    LBUL_1455 S-Adenosylmethionine synthetase 1.08 0.68 1.98 0.63
    LBUL_1554 Cysteinyl-tRNA synthetase 0.53 0.75 0.35 1.30
    str0083 cysE1 Serine acetyltransferase 0.69 0.76 1.59 0.56
    str0084 cysS Cysteinyl-tRNA synthetase 0.79 0.74 1.86 0.73
    str0352 metB1 Cystathionine gamma-synthase 0.09 0.02 1.27 0.05
    str0366 cysM1 Cysteine synthase 0.44 0.10 0.88 0.31
    str0451 metG Methionine-tRNA ligase 1.12 0.83 1.33 0.37
    str0566 pfs 5′-Methylthioadenosine/S-adenosylhomocysteine nucleosidase 0.49 0.94 2.91 1.59
    str0584 mmuM Homocysteine methyltransferase 0.40 0.45 1.42 0.32
    str0846 cysM2 Cysteine synthase 1.73 0.69 1.56 0.42
    str0847 metB2 Cystathionine beta-lyase 1.17 0.68 0.91 0.86
    str0848 cysE2 Serine acetyltransferase, putative 1.48 0.61 1.53 1.13
    str0987 cysD O-Acetylhomoserine sulfhydrylase 0.28 0.20 3.24 0.09
    str1172 metK S-Adenosylmethionine synthetase 0.40 0.57 1.52 0.06
    str1222 metA Homoserine O-succinyltransferase 0.28 0.26 1.49 0.13
Other amino acid and carbon dioxide metabolism
    LBUL_1105 Subtilisin-like serine protease prtB 0.45 0.42 8.89 0.42
    str1658 cah Carbonate dehydratase 15.75 3.73 0.71 0.92
ROS production and iron metabolism
    LBUL_2034 Acetolactate synthase pyruvate dehydrogenase, (cytochrome) glyoxylate carboligase phosphonopyruvate decarboxylase 0.44 0.24 0.80 11.11
    LBUL_1241 Translation initiation factor 2 (IF-2; GTPase) 2.29 2.19 3.48 1.22
    LBUL_1955 Dihydroorotate dehydrogenase 0.94 1.04 2.60 1.10
    str1025 fatB Ferrichrome ABC transporter, substrate-binding protein 0.83 0.90 4.34 0.59
    str1026 fatA Ferrichrome ABC transporter, ATP-binding protein 0.66 1.00 4.52 0.54
    str1027 fatC Ferrichrome ABC transporter, permease protein 0.74 0.96 3.95 0.34
    str1028 fatD Ferrichrome ABC transporter, permease protein 0.77 0.95 2.74 0.09
    str0723 dpr Peroxide resistance protein, non-heme iron-containing ferritin 1.48 0.76 0.35 1.22
    str0724 fur Ferric transport regulator protein 1.37 1.13 0.42 1.51
Fatty acid metabolism
    LBUL_0106 1-Acyl-sn-glycerol-3-phosphate acyltransferase 1.37 0.53 3.13 1.40
    LBUL_0109 1-Acyl-sn-glycerol-3-phosphate acyltransferase 0.63 0.62 4.76 0.91
    LBUL_0314 Phosphopantetheinyl transferase (holo-ACP synthase) 0.86 0.73 0.66 0.99
    LBUL_0818 3-Oxoacyl-(acyl-carrier-protein) 1.67 0.37 0.26 0.20
    LBUL_0819 Acyl carrier protein 1.49 0.84 0.32 0.41
    LBUL_0820 (Acyl-carrier-protein) S-malonyltransferase 1.44 0.28 0.19 0.27
    LBUL_0821 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) 1.66 0.33 0.26 0.20
    LBUL_0822 3-Oxoacyl-(acyl-carrier-protein) synthase 1.68 0.33 0.22 0.22
    LBUL_0823 Biotin carboxyl carrier protein 0.97 0.41 0.21 0.34
    LBUL_0824 3-Hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases 1.27 0.29 0.29 0.47
    LBUL_0825 Acetyl/propionyl-CoAb carboxylase alpha subunit 0.98 0.30 0.13 0.39
    LBUL_0826 Acetyl-CoA carboxylase beta subunit 0.94 0.28 0.24 0.28
    LBUL_0827 Acetyl-CoA carboxylase alpha subunit 1.36 0.26 0.60 0.37
    LBUL_0828 Enoyl-(acyl-carrier-protein) 0.90 0.30 0.10 0.32
    LBUL_0829 Biotin-(acetyl-CoA carboxylase) ligase 0.79 0.26 0.30 0.28
    LBUL_1256 1-Acyl-sn-glycerol-3-phosphate acyltransferase 1.09 0.35 1.55 14.99
    LBUL_1294 Acyl carrier protein 0.88 1.00 0.29 1.78
    LBUL_1356 Cyclopropane fatty acid synthase and related methyltransferases 0.77 0.41 0.52 0.05
    LBUL_1567 Biotin carboxylase 1.64 0.98 3.59 0.76
    LBUL_1568 Biotin carboxylase 0.88 0.49 1.29 0.36
    LBUL_1607 3-Hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases 0.60 0.44 0.71 4.36
a

Numbers indicate the ratios of differential expression of a gene in the mixed culture compared to the monoculture. Numbers in boldface have a ratio >2 or <0.5 and are significant (P = 0.05).

b

CoA, coenzyme A.